Publications for All Faculty

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Grant SS, Wellington S, Kawate T, Desjardins CA, Silvis MR, Wivagg C, Thompson M, Gordon K, Kazyanskaya E, Nietupski R, Haseley N, Iwase N, Earl AM, Fitzgerald M, Hung DT

Baeyer-Villiger Monooxygenases EthA and MymA Are Required for Activation of Replicating and Non-replicating Mycobacterium tuberculosis Inhibitors.
Cell Chem Biol. 2016;23(6):666-77 - PMID: 27321573 - PMCID: PMC4920728 - DOI: 10.1016/j.chembiol.2016.05.011

Zhou C, Elia AE, Naylor ML, Dephoure N, Ballif BA, Goel G, Xu Q, Ng A, Chou DM, Xavier RJ, Gygi SP, Elledge SJ

Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks.
Proc Natl Acad Sci U S A. 2016;113(26):E3667-75 - PMID: 27298372 - PMCID: PMC4932963 - DOI: 10.1073/pnas.1602827113

Boada-Romero E, Serramito-Gómez I, Sacristán MP, Boone DL, Xavier RJ, Pimentel-Muiños FX

The T300A Crohn's disease risk polymorphism impairs function of the WD40 domain of ATG16L1.
Nat Commun. 2016;7:11821 - PMID: 27273576 - PMCID: PMC4899871 - DOI: 10.1038/ncomms11821

Lassen KG, McKenzie CI, Mari M, Murano T, Begun J, Baxt LA, Goel G, Villablanca EJ, Kuo SY, Huang H, Macia L, Bhan AK, Batten M, Daly MJ, Reggiori F, Mackay CR, Xavier RJ

Genetic Coding Variant in GPR65 Alters Lysosomal pH and Links Lysosomal Dysfunction with Colitis Risk.
Immunity. 2016;44(6):1392-1405 - PMID: 27287411 - PMCID: PMC4936415 - DOI: 10.1016/j.immuni.2016.05.007

Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, , Xavier RJ

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.
Cell. 2016;165(6):1551 - PMID: 27259157 - DOI: 10.1016/j.cell.2016.05.056

Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, Lander ES, Knip M, , Xavier RJ

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability.
Sci Transl Med. 2016;8(343):343ra81 - PMID: 27306663 - PMCID: PMC5032909 - DOI: 10.1126/scitranslmed.aad0917

Saha SK, Gordan JD, Kleinstiver BP, Vu P, Najem MS, Yeo JC, Shi L, Kato Y, Levin RS, Webber JT, Damon LJ, Egan RK, Greninger P, McDermott U, Garnett MJ, Jenkins RL, Rieger-Christ KM, Sullivan TB, Hezel AF, Liss AS, Mizukami Y, Goyal L, Ferrone CR, Zhu AX, Joung JK, Shokat KM, Benes CH, Bardeesy N

Isocitrate dehydrogenase mutations confer dasatinib hypersensitivity and SRC-dependence in intrahepatic cholangiocarcinoma.
Cancer Discov. 2016;6(7):727-39 - PMID: 27231123 - PMCID: PMC5458737 - DOI: 10.1158/2159-8290.CD-15-1442

Pedamallu CS, Bhatt AS, Bullman S, Fowler S, Freeman SS, Durand J, Jung J, Duke F, Manzo V, Cai D, Ananthakrishnan A, Ojesina AI, Ramachandran A, Gevers D, Xavier RJ, Bhan AK, Meyerson M, Yajnik V

Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn's Disease.
Cell Mol Gastroenterol Hepatol. 2016;2(5):563-566.e5 - PMID: 28174737 - PMCID: PMC5042890 - DOI: 10.1016/j.jcmgh.2016.05.011

Sundberg TB, Liang Y, Wu H, Choi HG, Kim ND, Sim T, Johannessen L, Petrone A, Khor B, Graham DB, Latorre IJ, Phillips AJ, Schreiber SL, Perez J, Shamji AF, Gray NS, Xavier RJ

Development of Chemical Probes for Investigation of Salt-Inducible Kinase Function In Vivo.
ACS Chem Biol. 2016;11(8):2105-11 - PMID: 27224444 - PMCID: PMC4992440 - DOI: 10.1021/acschembio.6b00217

O'Connell DJ, Kolde R, Sooknah M, Graham DB, Sundberg TB, Latorre IJ, Mikkelsen TS, Xavier RJ

Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.
Cell Syst. 2016;2(5):323-334 - PMID: 27211859 - PMCID: PMC5032147 - DOI: 10.1016/j.cels.2016.04.011

Frydman GH, Bendapudi PK, Marini RP, Vanderburg CR, Tompkins RG, Fox JG

Coagulation Biomarkers in Healthy Chinese-Origin Rhesus Macaques (Macaca mulatta).
J Am Assoc Lab Anim Sci. 2016;55(3):252-9 - PMID: 27177557 - PMCID: PMC4865685

Ueki R, Liu L, Kashiwagi S, Kaneki M, Khan M, Hirose M, Tompkins RG, Martyn JA, Yasuhara S

Role of Elevated Fibrinogen in Burn-Induced Mitochondrial Dysfunction: Protective Effects of Glycyrrhizin.
Shock. 2016;46(4):382-9 - PMID: 27172157 - PMCID: PMC5026541 - DOI: 10.1097/SHK.0000000000000602

Lamas B, Richard ML, Leducq V, Pham HP, Michel ML, Da Costa G, Bridonneau C, Jegou S, Hoffmann TW, Natividad JM, Brot L, Taleb S, Couturier-Maillard A, Nion-Larmurier I, Merabtene F, Seksik P, Bourrier A, Cosnes J, Ryffel B, Beaugerie L, Launay JM, Langella P, Xavier RJ, Sokol H

CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands.
Nat Med. 2016;22(6):598-605 - PMID: 27158904 - PMCID: PMC5087285 - DOI: 10.1038/nm.4102

Chu H, Khosravi A, Kusumawardhani IP, Kwon AH, Vasconcelos AC, Cunha LD, Mayer AE, Shen Y, Wu WL, Kambal A, Targan SR, Xavier RJ, Ernst PB, Green DR, McGovern DP, Virgin HW, Mazmanian SK

Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease.
Science. 2016;352(6289):1116-20 - PMID: 27230380 - PMCID: PMC4996125 - DOI: 10.1126/science.aad9948

Taleban S, Stewart KO, Li DK, Singh P, Pardi DS, Sturgeon HC, Yajnik V, Xavier RJ, Ananthakrishnan AN, Khalili H

Clinical Activity and Quality of Life Indices Are Valid Across Ulcerative Colitis But Not Crohn's Disease Phenotypes.
Dig Dis Sci. 2016;61(9):2627-35 - PMID: 27142671 - PMCID: PMC4982770 - DOI: 10.1007/s10620-016-4180-8

Tsai SQ, Topkar VV, Joung JK, Aryee MJ

Open-source guideseq software for analysis of GUIDE-seq data.
Nat Biotechnol. 2016;34(5):483 - PMID: 27153277 - DOI: 10.1038/nbt.3534

Peloquin JM, Goel G, Villablanca EJ, Xavier RJ

Mechanisms of Pediatric Inflammatory Bowel Disease.
Annu Rev Immunol. 2016;34:31-64 - PMID: 27168239 - DOI: 10.1146/annurev-immunol-032414-112151

Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA, , Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.
Science. 2016;352(6285):565-9 - PMID: 27126040 - PMCID: PMC5240844 - DOI: 10.1126/science.aad3369

Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, DIABIMMUNE Study Group, Xavier RJ

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.
Cell. 2016;165(4):842-53 - PMID: 27133167 - PMCID: PMC4950857 - DOI: 10.1016/j.cell.2016.04.007

Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, , Xavier RJ

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.
Cell. 2016;165(4):842-53 - PMID: 27133167 - PMCID: PMC4950857 - DOI: 10.1016/j.cell.2016.04.007

Prywes N, Michaels YS, Pal A, Oh SS, Szostak JW

Thiolated uridine substrates and templates improve the rate and fidelity of ribozyme-catalyzed RNA copying.
Chem Commun (Camb). 2016;52(39):6529-32 - PMID: 27109314 - DOI: 10.1039/c6cc02692c

Netea MG, Joosten LA, Latz E, Mills KH, Natoli G, Stunnenberg HG, O'Neill LA, Xavier RJ

Trained immunity: A program of innate immune memory in health and disease.
Science. 2016;352(6284):aaf1098 - PMID: 27102489 - PMCID: PMC5087274 - DOI: 10.1126/science.aaf1098

Zimmer S, Grebe A, Bakke SS, Bode N, Halvorsen B, Ulas T, Skjelland M, De Nardo D, Labzin LI, Kerksiek A, Hempel C, Heneka MT, Hawxhurst V, Fitzgerald ML, Trebicka J, Björkhem I, Gustafsson JÅ, Westerterp M, Tall AR, Wright SD, Espevik T, Schultze JL, Nickenig G, Lütjohann D, Latz E

Cyclodextrin promotes atherosclerosis regression via macrophage reprogramming.
Sci Transl Med. 2016;8(333):333ra50 - PMID: 27053774 - PMCID: PMC4878149 - DOI: 10.1126/scitranslmed.aad6100

Tsai SQ, Joung JK

Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases.
Nat Rev Genet. 2016;17(5):300-12 - PMID: 27087594 - PMCID: PMC7225572 - DOI: 10.1038/nrg.2016.28

Abrams JA, Xavier RJ, Rustgi AK

Timothy C. Wang, MD: Our next AGA President.
Gastroenterology. 2016;150(5):1231-1236 - PMID: 27018487 - DOI: 10.1053/j.gastro.2016.03.021
Total: 2498